In a large pot of simmering water, boil the potatoes just until tender. Drain and set aside.
In a large, heavy-bottomed saucepot, saute the diced onion, carrot and celery in 2 tablespoons butter until vegetables are softened, stirring constantly to avoid coloring. Add the water and bring to a boil.
Reduce to a simmer and whisk in the fish base. Add the potatoes, cream, dill, thyme and pepper.
In a separate pan (what, another one?!?), melt the remaining 1/4 cup butter over medium heat. Add the flour, stirring constantly, and cook for 2 to 4 minutes to make a roux.
Whisk the roux into the chowder and continue to cook until thickened over medium high heat, approximately 2 to 4 minutes after the mixture has reached a boil.
Add the fish, shrimp and scallops to the chowder just before serving, and simmer until the seafood is fully cooked, about 5 minutes. Season with salt and pepper to taste.